Databases

Question 1

Uniprot

Answer 1

protein

Question 2

EMBL

Answer 2

gene

Question 3

ENSEMBL

Answer 3

genome

Question 4

NCBI

Answer 4

bacteria

Question 5

methods for sequence comparison

Answer 5

1. Diagonal plots
2. FASTA
3. BLAST

Question 6

FASTA

Answer 6

speeding up alignments with hash tables, heuristic algorithm, usage of K-tuples to search for matching sequence patterns of K-tuple hits

Question 7

BLAST

Answer 7

an algorithm for comparing primary biological sequence information, optimized for speed use.

Question 8

blastn

Answer 8

compares your nucleotide sequence with database nucleotide sequence

Question 9

blastp

Answer 9

compares your query protein sequence with database of protein sequence that were derived from cDNA of interest

Question 10

blastx

Answer 10

first translates your sequence into amino acids in 6 reading frames then compares the protein sequences with protein databases

Question 11

tblastn

Answer 11

compares your query protein sequence with the database after translating each nucleotide sequence into protein using all 6 reading frames

Question 12

tblastx

Answer 12

translates both query nucleotide sequence & the database sequence in all 6 reading frames & then compares the protein sequence. looks for protein coding regions. Good choice- less noise

Question 13

PROSITE

Answer 13

protein database. Its uses includes identifying possible functions of newly discovered proteins and analysis of known proteins for previously undetermined activity

Question 14

what is PSI-BLAST

Answer 14

(position specific iterated BLAST)- iterative search using protein BLAST algorithm.

Question 15

how is PSI-BLAST used

Answer 15

1. a list of all closely related proteins is created
2. these proteins are combined into a general “profile” sequence, which summarizes significant features present in their sequences
3. a query against the protein database is then run using this profile. larger group of proteins is found
4. this larger group- used to construct another profile-> process repeated

Question 16

HMMR

Answer 16

software for working with sequence HMM (hidden markov models= generalization of protein models).

Question 17

Pfam

Answer 17

protein family database. looks at domains & protein family definitions & HMM

Question 18

MFFT & Clustal Omega

Answer 18

MSA program for amino acids or nucleotide sequence

Question 19

programs for phylogenetic tree constructions

Answer 19

1. clustal w: distance method
2. Phylip/protpars: parsimony
3. Tree, PaPa: progressive alignment, followed by parsimony

Question 20

PDB (protein data bank)

Answer 20

s a repository for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids

Question 21

PDB contents

Answer 21

x-ray structures
NMR structures
EM models
Models from predictions/modelling

Question 22

3D structures (proteins) databases 
- hierarchal fold classification

Answer 22

SCOP (annotaed)
CATH (automated)
= both have classes, fold, superfamily, family

Question 23

PROSITE & Pfram

Answer 23

sequence based classification of protein domains, families

Question 24

ENZYME

Answer 24

enzyme nomenclature

Question 25

BRENDA

Answer 25

nomenclature, isolation & purification, stability etc

Question 26

KEGG

Answer 26

resource for understanding high level functions & utilities of the biological system

Question 27

Programs defining secondary structures (protiens)

Answer 27

PSI-PRED

Question 28

Predicting simple sequence features (proteins)

Answer 28

``` Signal P ( signal peptide) Target P (cellular localisation) ```

Question 29

Ab initio homology modelling

Answer 29

Rosetta: generate the model by adding fragments together

Question 30

software/tools for systems biology

Answer 30

1. obtaining data sets from databases ( TCGA, cBioPortal) 2. first analysis of data sets based on gene expression- MultiExp 3. Networks- String, IMP 4. Pathway analysis: PANTHER, DAVID, KEGG 5. Metacore

Question 31

HADDOCK

Answer 31

high ambiguity driven protein-protein docking | -> use of biochemical and/or biophysical interaction data

Question 32

SwissPro

Answer 32

reviewed manually. high quality manually annotated & non-redundant protein sequence database

Question 33

TrEMBL

Answer 33

unreviewed. contains protein sequences associated with computational generated annotation & large scale functional characterization